Viruses, bacterial, yeast and eukaryotic multicellular organisms may coexist in complex associations in nature. An example of this type of association is that of microbiomes, which inhabit mammalian hosts. Rapid DNA sequencing techniques have been used to investigate microbiomes. The accuracy of the species identification has been adversely affected by uncertainty concerning the presence and amount of mammalian genomic DNA in the samples that affect the signal to noise ratio. This is particularly problematic in those situations where the DNA of interest is present in very small amounts amidst a high background of host genomic material.
Zhigang Wu, et al. (Lab Chip, 9:1193-1199 (2009)) developed a microfluidic device to physically separate bacterial cells from human blood cells based on soft inertial force-induced migration using flow-defined, curved and focused sample flow inside a microfluidic device resulting in 300-fold enrichment of bacteria. This type of cell separation can only reduce background contamination of the DNA between two types of cells if the cells are viable.
Another method used to isolate DNA from sepsis-causative bacteria in blood relies on the selective lysis of human-nucleated cells using a chaotropic reagent (MolYsis, Molzym GmbH, Bremen, Germany). This method also relies on viable cells. A salt-resistant DNase was used to degrade human DNA from lyzed cells, while intact bacterial cells were unaffected by DNAse. The DNAse was then inactivated and the bacterial DNA extracted and purified for analysis. The technique reduces the total human DNA concentration in the sample by 99.5%. However, total bacterial DNA recovery was low at only 30% of the expected total (Horz, et al., Anaerobe 16:47-53 (2010)).
At present, there is no satisfactory method for enriching target DNA from an environmental sample, which contains a mixture of DNAs under conditions in which loss of target DNA is minimized and viable cells as a source of DNA are not a requirement.